Tissue-specific BMAL1 cistromes reveal that rhythmic transcription is associated with rhythmic enhancer–enhancer interactions

JR Beytebiere, AJ Trott, BJ Greenwell… - Genes & …, 2019 - genesdev.cshlp.org
The mammalian circadian clock relies on the transcription factor CLOCK: BMAL1 to
coordinate the rhythmic expression of thousands of genes. Consistent with the various …

Prioritizing candidate disease miRNAs by topological features in the miRNA target–dysregulated network: Case study of prostate cancer

J Xu, CX Li, JY Lv, YS Li, Y **ao, TT Shao… - Molecular cancer …, 2011 - aacrjournals.org
Abstract Recently, microRNAs (miRNA), small noncoding RNAs, have taken center stage in
the field of human molecular oncology. However, their roles in tumor biology remain largely …

A deep learning model to identify gene expression level using cobinding transcription factor signals

L Zhang, Y Yang, L Chai, Q Li, J Liu… - Briefings in …, 2022 - academic.oup.com
Gene expression is directly controlled by transcription factors (TFs) in a complex
combination manner. It remains a challenging task to systematically infer how the …

[HTML][HTML] Full-Length Transcriptome Survey and Expression Analysis of Cassia obtusifolia to Discover Putative Genes Related to Aurantio-Obtusin Biosynthesis, Seed …

Y Deng, H Zheng, Z Yan, D Liao, C Li, J Zhou… - International Journal of …, 2018 - mdpi.com
The seed is the pharmaceutical and breeding organ of Cassia obtusifolia, a well-known
medical herb containing aurantio-obtusin (a kind of anthraquinone), food, and landscape. In …

Cooperation of ATF4 and CTCF promotes adipogenesis through transcriptional regulation

Y Chen, R He, Z Han, Y Wu, Q Wang, X Zhu… - Cell biology and …, 2022 - Springer
Adipogenesis is a multi-step process orchestrated by activation of numerous TFs, whose
cooperation and regulatory network remain elusive. Activating transcription factor 4 (ATF4) is …

Transcriptional regulation of CYP2C19 and its role in altered enzyme activity

C Rao S. Uppugunduri, Y Daali… - Current drug …, 2012 - benthamdirect.com
Cytochrome P450 2C19 (CYP2C19) is involved in the metabolism of several drugs that are
currently in clinical use. The gene encoding CYP2C19 is polymorphic with the existence of …

Revealing transcription factor and histone modification co-localization and dynamics across cell lines by integrating ChIP-seq and RNA-seq data

L Zhang, G Xue, J Liu, Q Li, Y Wang - BMC genomics, 2018 - Springer
Background Interactions among transcription factors (TFs) and histone modifications (HMs)
play an important role in the precise regulation of gene expression. The context specificity of …

Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues

L Steuernagel, C Meckbach, F Heinrich, S Zeidler… - PLoS …, 2019 - journals.plos.org
Transcription factors (TFs) are a special class of DNA-binding proteins that orchestrate gene
transcription by recruiting other TFs, co-activators or co-repressors. Their combinatorial …

Predictive models of spatial transcriptional response to high salinity

S Uygun, AE Seddon, CB Azodi, SH Shiu - Plant physiology, 2017 - academic.oup.com
Plants are exposed to a variety of environmental conditions, and their ability to respond to
environmental variation depends on the proper regulation of gene expression in an organ …

PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information

C Meckbach, R Tacke, X Hua, S Waack… - BMC …, 2015 - Springer
Abstract Background Transcription factors (TFs) are important regulatory proteins that
govern transcriptional regulation. Today, it is known that in higher organisms different TFs …